Branch: rosetta:commits 「revision: №20469」
Test: linux.clang.python310.PyRosetta.unit
SubTest: T200_Scoring
SubTest files: 「file-system-view」
Daemon: hojo-3    
State: T200_Scoring

core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+5.HEAD.c9abca8 c9abca83f0a4dd927aceaa98f4ceeb8708e10f37 git@github.com:RosettaCommons/rosetta.git 2024-09-07T17:30:08 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.17/clang-3.4.2/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.34 seconds. core.import_pose.import_pose: File '../test/data/test_fragments.pdb' automatically determined to be of type PDB core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ALA:CtermProteinFull 10 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.17/clang-3.4.2/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.17/clang-3.4.2/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.22 seconds to load from binary basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt basic.io.database: Database file opened: scoring/score_function┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+5.HEAD.c9abca83f0a4dd927aceaa98f4ceeb8708e10f37 2024-09-07T17:30:08] retrieved from: git@github.com:RosettaCommons/rosetta.git Scoring ---------------------------------------------- Creating standard fullatom score function and scoring Creating standard centroid score function and scoring Creating standard score function and scoring, again Creating standard score from scratch Adjusting weights and scoring weight for fa_atr set to: 1.0 ScoreFunction::show(): weights: (fa_atr 1) (fa_rep 1) (fa_pair 1) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: EnergyMethodOptions::show: mhc_epitope_setup_files: EnergyMethodOptions::show: netcharge_setup_files: EnergyMethodOptions::show: aspartimide_penalty_value: 25 EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid EnergyMethodOptions::show: covalent_labeling_input: EnergyMethodOptions::show: covalent_labeling_fa_input: EnergyMethodOptions::show: hrf_dynamics_input: EnergyMethodOptions::show: depc_ms_input: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false EnergyMethodOptions::show: exclude_monomer_fa_elec: false EnergyMethodOptions::show: elec_max_dis: 5.5 EnergyMethodOptions::show: elec_min_dis: 1.6 EnergyMethodOptions::show: elec_die: 10 EnergyMethodOptions::show: elec_no_dis_dep_die: false EnergyMethodOptions::show: elec_sigmoidal_die: true EnergyMethodOptions::show: elec_sigmoidal_D: 80 EnergyMethodOptions::show: elec_sigmoidal_D0: 6 EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 EnergyMethodOptions::show: smooth_fa_elec: true EnergyMethodOptions::show: grpelec_fade_type: false EnergyMethodOptions::show: grpelec_fade_param1: 1 EnergyMethodOptions::show: grpelec_fade_param2: 1 EnergyMethodOptions::show: grpelec_fade_hbond: 0 EnergyMethodOptions::show: grp_cpfxn: 1 EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat EnergyMethodOptions::show: grpelec_context_dependent: 0 EnergyMethodOptions::show: use_polarization: true EnergyMethodOptions::show: use_gen_kirkwood: true EnergyMethodOptions::show: protein_dielectric: 1 EnergyMethodOptions::show: water_dielectric: 78.3 EnergyMethodOptions::show: exclude_DNA_DNA: false EnergyMethodOptions::show: exclude_intra_res_protein: true EnergyMethodOptions::show: count_pair_hybrid: false EnergyMethodOptions::show: count_pair_full: false EnergyMethodOptions::show: put_intra_into_total: false EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true EnergyMethodOptions::show: eval_intrares_elec_ST_only: false EnergyMethodOptions::show: envsmooth_zero_negatives: false EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 EnergyMethodOptions::show: pb_bound_tag: bound EnergyMethodOptions::show: pb_unbound_tag: unbound EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1 EnergyMethodOptions::show: ordered_wat_penalty: 1.221 EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 EnergyMethodOptions::show: nmer_ref_seq_length_: 9 EnergyMethodOptions::show: nmer_svm_term_length_: 3 EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 EnergyMethodOptions::show: nmer_svm_scorecut_: 0 EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 EnergyMethodOptions::show: nmer_svm_aa_matrix_: EnergyMethodOptions::show: nmer_svm_list_defined_: 0 EnergyMethodOptions::show: nmer_svm_list_: EnergyMethodOptions::show: nmer_svm_defined_: 0 EnergyMethodOptions::show: nmer_svm_: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 EnergyMethodOptions::show: nmer_svm_rank_list_: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 EnergyMethodOptions::show: nmer_svm_rank_: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" EnergyMethodOptions::show: hbnet_max_network_size_: 0 EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0 EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0 EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0 EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0 EnergyMethodOptions::show: target_clash_pdb_: EnergyMethodOptions::show: dump_trajectory_prefix_: traj EnergyMethodOptions::show: dump_trajectory_gz_: FALSE EnergyMethodOptions::show: dump_trajectory_stride_: 1 EnergyMethodOptions::show: bond_angle_central_atoms_to_score: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none HBondOptions::show: hb_max_energy: 0 HBondOptions::show: exclude_DNA_DNA: false HBondOptions::show: exclude_intra_res_protein_: true HBondOptions::show: exclude_intra_res_RNA_: false HBondOptions::show: put_intra_into_total_: false HBondOptions::show: exclude_self_hbonds: true HBondOptions::show: use_hb_env_dep: true HBondOptions::show: use_hb_env_dep_DNA: true HBondOptions::show: smooth_hb_env_dep: true HBondOptions::show: bb_donor_acceptor_check: true HBondOptions::show: decompose_bb_hb_into_pair_energies: false HBondOptions::show: params_database_tag_: ref2015_params HBondOptions::show: use_sp2_chi_penalty_: true HBondOptions::show: sp2_BAH180_rise_: 0.75 HBondOptions::show: sp2_outer_width_: 0.357 HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true HBondOptions::show: fade_energy_: 1 HBondOptions::show: exclude_ether_oxygens_: 0 HBondOptions::show: Mbhbond: false HbondOptions::show: mphbond: false HBondOptions::show: hbond_energy_shift: 0 HBondOptions::show: water_hybrid_sf: false RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat FreeDOF_Options::show: free_suite_bonus: -1 FreeDOF_Options::show: free_2HOprime_bonus: -0.5 FreeDOF_Options::show: free_sugar_bonus: -1 FreeDOF_Options::show: pack_phosphate_penalty: 0.25 FreeDOF_Options::show: free_side_chain_bonus: -0.5 Score break down for pose... all residue energies are None weighted energies for residue 5 None fa_atr: -0.593 fa_rep: 0.118 fa_pair: 0.000 fa_atr of residue 5 -0.5929040959214456 fa_atr for residue 5: -0.5929040959214456 manually calculating 2body context-independent energies between residues 4 and 5 fa_atr between 1 and 2: -0.42118788604496193 fa_pair between 1 and 2: 0.0 fa_rep between 1 and 2: 0.12092691972750393 ScoreType.fa_atrScoreType.fa_repScoreType.fa_solScoreType.fa_intra_atrScoreType.fa_intra_repScoreType.fa_intra_solScoreType.fa_intra_atr_xover4ScoreType.fa_intra_rep_xover4ScoreType.fa_intra_sol_xover4ScoreType.fa_intra_atr_nonproteinScoreType.fa_intra_rep_nonproteinScoreType.fa_intra_sol_nonproteinScoreType.fa_intra_RNA_base_phos_atrScoreType.fa_intra_RNA_base_phos_repScoreType.fa_intra_RNA_base_phos_solScoreType.fa_atr_dummyScoreType.fa_rep_dummyScoreType.fa_sol_dummyScoreType.fa_vdw_tinkerScoreType.lk_hackScoreType.lk_ballScoreType.lk_ball_wtdScoreType.lk_ball_isoScoreType.lk_ball_bridgeScoreType.lk_ball_bridge_uncplScoreType.lk_domeScoreType.lk_dome_isoScoreType.lk_dome_bridgeScoreType.lk_dome_bridge_uncplScoreType.lk_ball_bridge2ScoreType.lk_ball_bridge_uncpl2ScoreType.lk_dome_packScoreType.coarse_fa_atrScoreType.coarse_fa_repScoreType.coarse_fa_solScoreType.coarse_beadljScoreType.mm_lj_intra_repScoreType.mm_lj_intra_atrScoreType.mm_lj_inter_repScoreType.mm_lj_inter_atrScoreType.mm_twistScoreType.mm_bendScoreType.mm_stretchScoreType.lk_costhetaScoreType.lk_polarScoreType.lk_nonpolarScoreType.lk_polar_intra_RNAScoreType.lk_nonpolar_intra_RNAScoreType.fa_elecScoreType.fa_elec_bb_bbScoreType.fa_elec_bb_scScoreType.fa_elec_sc_scScoreType.fa_intra_elecScoreType.fa_imm_elecScoreType.h2o_hbondScoreType.dna_drScoreType.dna_bpScoreType.dna_bsScoreType.dna_refScoreType.peptide_bondScoreType.pcsScoreType.pcsTs1ScoreType.pcsTs2ScoreType.pcsTs3ScoreType.pcsTs4ScoreType.pcs2ScoreType.fastsaxsScoreType.saxs_scoreScoreType.saxs_cen_scoreScoreType.saxs_fa_scoreScoreType.pddf_scoreScoreType.fiberdiffractionScoreType.fiberdiffractiondensScoreType.epr_deer_scoreScoreType.fa_mbenvScoreType.fa_mbsolvScoreType.fa_elec_rna_phos_phosScoreType.fa_elec_rna_phos_sugrScoreType.fa_elec_rna_phos_baseScoreType.fa_elec_rna_sugr_sugrScoreType.fa_elec_rna_sugr_baseScoreType.fa_elec_rna_base_baseScoreType.fa_elec_rna_phos_phos_fastScoreType.fa_elec_rna_phos_sugr_fastScoreType.fa_elec_rna_phos_base_fastScoreType.fa_elec_rna_sugr_sugr_fastScoreType.fa_elec_rna_sugr_base_fastScoreType.fa_elec_rna_base_base_fastScoreType.fa_elec_aro_aroScoreType.fa_elec_aro_allScoreType.hack_aroScoreType.rna_fa_atr_baseScoreType.rna_fa_rep_baseScoreType.rna_data_backboneScoreType.ch_bondScoreType.ch_bond_bb_bbScoreType.ch_bond_sc_scScoreType.ch_bond_bb_scScoreType.pro_closeScoreType.rama2bScoreType.vdwScoreType.cenpackScoreType.cenpack_smoothScoreType.cen_hbScoreType.hybrid_vdwScoreType.gaussScoreType.rna_vdwScoreType.rnp_vdwScoreType.rna_base_backboneScoreType.rna_backbone_backboneScoreType.rna_repulsiveScoreType.rna_base_pair_pairwiseScoreType.rna_base_axis_pairwiseScoreType.rna_base_stagger_pairwiseScoreType.rna_base_stack_pairwiseScoreType.rna_base_stack_axis_pairwiseScoreType.rna_data_baseScoreType.rna_base_pairScoreType.rna_base_axisScoreType.rna_base_staggerScoreType.rna_base_stackScoreType.rna_base_stack_axisScoreType.rnp_base_pairScoreType.rnp_stackScoreType.rnp_stack_xyScoreType.rnp_pairScoreType.rnp_pair_distScoreType.rnp_aa_to_rna_backboneScoreType.rna_mg_pointScoreType.rna_mg_point_indirectScoreType.mgScoreType.mg_ligScoreType.mg_solScoreType.mg_refScoreType.hoh_refScoreType.rna_torsionScoreType.rna_torsion_scScoreType.rna_suiteScoreType.rna_jr_suiteScoreType.suiteness_bonusScoreType.tna_suiteScoreType.rna_sugar_closeScoreType.fa_stackScoreType.fa_stack_lowerScoreType.fa_stack_upperScoreType.fa_stack_aroScoreType.fa_stack_extScoreType.fa_stack_solScoreType.fa_stack_lrScoreType.fa_stack_rna_proteinScoreType.fa_stack_rna_protein_aroScoreType.ss_contact_worstScoreType.stack_elecScoreType.stack_elec_base_baseScoreType.stack_elec_base_bbScoreType.alignmentScoreType.dna_bb_torsionScoreType.dna_sugar_closeScoreType.dna_base_distanceScoreType.geom_sol_fastScoreType.geom_sol_fast_intra_RNAScoreType.fa_cust_pair_distScoreType.custom_atom_pairScoreType.orbitals_hpol_bbScoreType.pci_cation_piScoreType.pci_pi_piScoreType.pci_salt_bridgeScoreType.pci_hbondScoreType.arg_cation_piScoreType.PyRosettaTwoBodyContextIndepenedentEnergy_firstScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.PyRosettaTwoBodyContextIndepenedentEnergy_lastScoreType.pythonScoreType.fa_pairScoreType.fa_pair_aro_aroScoreType.fa_pair_aro_polScoreType.fa_pair_pol_polScoreType.hbond_sr_bbScoreType.hbond_lr_bbScoreType.hbond_bb_scScoreType.hbond_sr_bb_scScoreType.hbond_lr_bb_scScoreType.hbond_scScoreType.hbond_intraScoreType.hbond_watScoreType.wat_entropyScoreType.hbondScoreType.npd_hbond_sr_bbScoreType.npd_hbond_lr_bbScoreType.npd_hbond_bb_scScoreType.npd_hbond_sr_bb_scScoreType.npd_hbond_lr_bb_scScoreType.npd_hbond_scScoreType.npd_hbond_intraScoreType.npd_hbondScoreType.fa_grpelecScoreType.PyRosettaTwoBodyContextDependentEnergy_firstScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.PyRosettaTwoBodyContextDependentEnergy_lastScoreType.interface_dd_pairScoreType.geom_solScoreType.geom_sol_intra_RNAScoreType.occ_sol_fittedScoreType.occ_sol_fitted_onebodyScoreType.occ_sol_exactScoreType.cen_rot_pairScoreType.cen_rot_pair_angScoreType.cen_rot_pair_dihScoreType.pairScoreType.cen_pair_smoothScoreType.MpairScoreType.MPPairScoreType.FaMPSolvScoreType.suckScoreType.rna_rgScoreType.rna_motifScoreType.facts_elecScoreType.facts_solvScoreType.facts_sasaScoreType.motif_dockScoreType.pointwaterScoreType.goapScoreType.goap_distScoreType.goap_angleScoreType.approximate_buried_unsat_penaltyScoreType.interchain_pairScoreType.interchain_vdwScoreType.gb_elecScoreType.multipole_elecScoreType.fa_sasaScoreType.dslf_ss_dstScoreType.dslf_cs_angScoreType.dslf_ss_dihScoreType.dslf_ca_dihScoreType.dslf_cbs_dsScoreType.dslf_fa13ScoreType.dslfc_cen_dstScoreType.dslfc_cb_dstScoreType.dslfc_angScoreType.dslfc_cb_dihScoreType.dslfc_bb_dihScoreType.dslfc_rotScoreType.dslfc_transScoreType.dslfc_RTScoreType.atom_pair_constraintScoreType.base_pair_constraintScoreType.coarse_chainbreak_constraintScoreType.constant_constraintScoreType.coordinate_constraintScoreType.angle_constraintScoreType.dihedral_constraintScoreType.big_bin_constraintScoreType.dunbrack_constraintScoreType.site_constraintScoreType.metalhash_constraintScoreType.metalbinding_constraintScoreType.rna_stub_coord_hackScoreType.bond_geometryScoreType.rna_bond_geometryScoreType.Hpol_bond_geometryScoreType.ramaScoreType.omegaScoreType.fa_dunScoreType.fa_dun_devScoreType.fa_dun_rotScoreType.fa_dun_semiScoreType.cen_rot_dunScoreType.dna_chiScoreType.p_aa_ppScoreType.p_aa_ssScoreType.yhh_planarityScoreType.hxl_torsScoreType.h2o_intraScoreType.refScoreType.ref_ncScoreType.seqdep_refScoreType.nmer_refScoreType.nmer_pssmScoreType.nmer_svmScoreType.envsmoothScoreType.e_pHScoreType.rna_bulgeScoreType.dna_dihedral_bbScoreType.dna_dihedral_chiScoreType.dna_dihedral_sugarScoreType.sugar_bbScoreType.free_suiteScoreType.free_2HOprimeScoreType.free_side_chainScoreType.free_baseScoreType.free_resScoreType.free_dofScoreType.intermolScoreType.other_poseScoreType.special_rotScoreType.PB_elecScoreType.cen_env_smoothScoreType.cbeta_smoothScoreType.cen_rot_envScoreType.cen_rot_cbetaScoreType.envScoreType.cbetaScoreType.DFIREScoreType.MenvScoreType.McbetaScoreType.Menv_non_helixScoreType.Menv_terminiScoreType.Menv_tm_projScoreType.MlipoScoreType.rgScoreType.rg_localScoreType.coScoreType.hs_pairScoreType.ss_pairScoreType.rsigmaScoreType.sheetScoreType.burial_v2ScoreType.burialScoreType.abegoScoreType.covalent_labelingScoreType.covalent_labeling_faScoreType.hrf_ms_labelingScoreType.hrf_dynamicsScoreType.ccs_immsScoreType.depc_msScoreType.rnp_envScoreType.loop_closeScoreType.missing_resScoreType.MPEnvScoreType.MPCbetaScoreType.MPLipoScoreType.MPTerminiScoreType.MPNonHelixScoreType.MPTMProjScoreType.FaMPEnvScoreType.FaMPEnvSmoothScoreType.fa_water_to_bilayerScoreType.f_elec_lipidlayerScoreType.FaMPAsymEzCBScoreType.FaMPAsymEzCGScoreType.MPResidueLipophilicityScoreType.span_insScoreType.mp_span_angScoreType.MPHelicalityScoreType.natbias_ssScoreType.natbias_hsScoreType.natbias_hhScoreType.natbias_stwistScoreType.aa_cmpScoreType.dock_ens_confScoreType.csaScoreType.dcScoreType.rdcScoreType.rdc_segmentsScoreType.rdc_rohlScoreType.nmr_pcsScoreType.nmr_rdcScoreType.nmr_preScoreType.cen_pair_motifsScoreType.cen_pair_motif_degreeScoreType.holesScoreType.holes_decoyScoreType.holes_reslScoreType.holes_minScoreType.holes_min_meanScoreType.rna_chem_shiftScoreType.rna_chem_mapScoreType.rna_chem_map_loresScoreType.rna_partitionScoreType.dab_sasaScoreType.dab_sevScoreType.saScoreType.d2h_saScoreType.ProQMScoreType.ProQScoreType.interchain_envScoreType.interchain_contactScoreType.chainbreakScoreType.linear_chainbreakScoreType.overlap_chainbreakScoreType.distance_chainbreaks/EnvPairPotential/pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt basic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.HS.resmooth basic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.SS.resmooth basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine core.scoring.ScoreFunction: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -5.202 -5.202 fa_rep 1.000 1.049 1.049 fa_pair 1.000 0.000 0.000 --------------------------------------------------- Total weighted score: -4.153 core.scoring.Energies: E fa_atr fa_rep fa_pair core.scoring.Energies: E(i) 1 -0.30 0.06 0.00 core.scoring.Energies: E(i) 2 -0.51 0.12 0.00 core.scoring.Energies: E(i) 3 -0.60 0.11 0.00 core.scoring.Energies: E(i) 4 -0.59 0.12 0.00 core.scoring.Energies: E(i) 5 -0.59 0.12 0.00 core.scoring.Energies: E(i) 6 -0.60 0.11 0.00 core.scoring.Energies: E(i) 7 -0.60 0.11 0.00 core.scoring.Energies: E(i) 8 -0.59 0.12 0.00 core.scoring.Energies: E(i) 9 -0.52 0.12 0.00 core.scoring.Energies: E(i) 10 -0.31 0.06 0.00 core.scoring.Energies: total_energy fa_atr -5.202 core.scoring.Energies: total_energy fa_rep 1.049 core.scoring.Energies: total_energy fa_pair 0.000 core.scoring.Energies: E fa_atr fa_rep fa_pair core.scoring.Energies: E(i) 5 -0.59 0.12 0.00 core.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.hbonds.HBondSet: #Dch Dn Dres Da Ach An Ares Aa length AHDang BAHang BAtor weight energy core.scoring.hbonds.HBondSet: #A 6 HIS N A 2 ALA O 2.04 144.3 129.5 -90.7 1.000 -0.591 core.scoring.hbonds.HBondSet: #A 8 ILE N A 4 THR O 2.02 165.0 165.8 -132.1 1.000 -1.102 core.scoring.hbonds.HBondSet: #A 9 LEU N A 5 ILE O 2.26 163.0 149.7 -108.0 1.000 -0.865 core.scoring.hbonds.HBondSet: #A 10 ASP N A 7 SER O 1.99 118.8 121.9 -72.7 1.000 -0.053 core.scoring.hbonds.HBondSet: #A 11 TRP N A 7 SER O 2.13 163.6 152.7 150.3 1.000 -1.338 core.scoring.hbonds.HBondSet: #A 12 ILE N A 8 ILE O 2.03 139.2 140.6 -123.7 1.000 -0.721 core.scoring.hbonds.HBondSet: #A 13 GLU N A 9 LEU O 2.04 165.1 162.3 -156.5 1.000 -1.224 core.scoring.hbonds.HBondSet: #A 14 ASP N A 10 ASP O 1.86 150.2 152.5 -107.8 1.000 -0.689 core.scoring.hbonds.HBondSet: #A 15 ASN ND2A 11 TRP O 1.74 167.5 145.0 55.4 0.576 -1.075 core.scoring.hbonds.HBondSet: #A 15 ASN N A 12 ILE O 1.90 129.6 117.0 -123.3 1.000 -0.502 core.scoring.hbonds.HBondSet: #A 16 LEU N A 12 ILE O 2.12 139.7 156.3 41.7 1.000 -0.648 core.scoring.hbonds.HBondSet: #A 51 TYR OH A 13 GLU OE1 2.33 127.5 132.6 175.2 0.694 -0.057 core.scoring.hbonds.HBondSet: #A 55 ARG NH1A 13 GLU OE2 1.34 170.5 131.0 -58.3 0.812 -0.243 core.scoring.hbonds.HBondSet: #A 18 SER N A 15 ASN O 2.25 125.4 126.6 135.8 1.000 -0.507 core.scoring.hbonds.HBondSet: #A 56 LYS NZ A 19 PRO O 2.09 136.2 127.1 -155.2 0.835 -0.338 core.scoring.hbonds.HBondSet: #A 26 SER N A 22 LEU O 1.89 153.1 161.7 -159.5 1.000 -0.965 core.scoring.hbonds.HBondSet: #A 27 GLU N A 23 GLU O 1.90 127.2 124.4 -127.4 1.000 -0.529 core.scoring.hbonds.HBondSet: #A 28 ARG N A 24 LYS O 2.13 151.6 161.0 139.1 1.000 -0.876 core.scoring.hbonds.HBondSet: #A 30 GLY N A 28 ARG O 2.49 110.6 116.7 -151.7 1.000 -0.033 core.scoring.hbonds.HBondSet: #A 35 HIS N A 32 SER OG 2.29 149.9 129.3 42.4 0.412 -1.133 core.scoring.hbonds.HBondSet: #A 36 LEU N A 32 SER O 2.00 150.7 167.4 51.1 1.000 -0.802 core.scoring.hbonds.HBondSet: #A 37 GLN N A 33 LYS O 2.10 152.4 144.0 -111.3 1.000 -0.862 core.scoring.hbonds.HBondSet: #A 38 ARG N A 34 TRP O 2.05 155.6 134.2 -129.9 1.000 -1.268 core.scoring.hbonds.HBondSet: #A 39 MET N A 35 HIS O 1.83 162.3 167.2 121.8 1.000 -0.888 core.scoring.hbonds.HBondSet: #A 40 PHE N A 36 LEU O 2.00 162.8 150.8 -90.5 1.000 -1.000 core.scoring.hbonds.HBondSet: #A 41 LYS N A 37 GLN O 1.92 156.7 151.5 -106.1 1.000 -0.897 core.scoring.hbonds.HBondSet: #A 42 LYS N A 38 ARG O 2.04 174.7 160.8 -124.7 1.000 -1.211 core.scoring.hbonds.HBondSet: #A 43 GLU N A 39 MET O 1.81 133.8 142.7 -148.9 1.000 -0.720 core.scoring.hbonds.HBondSet: #A 44 THR N A 40 PHE O 1.84 148.2 139.0 -104.0 1.000 -0.626 core.scoring.hbonds.HBondSet: #A 46 HIS N A 44 THR OG1 2.38 140.9 115.1 31.0 0.647 -0.563 core.scoring.hbonds.HBondSet: #A 51 TYR N A 47 SER O 2.31 143.2 157.6 -134.7 1.000 -0.475 core.scoring.hbonds.HBondSet: #A 52 ILE N A 48 LEU O 2.04 169.5 172.7 -140.4 1.000 -1.110 core.scoring.hbonds.HBondSet: #A 53 ARG N A 49 GLY O 2.27 160.5 141.5 -138.6 1.000 -1.219 core.scoring.hbonds.HBondSet: #A 54 SER N A 50 GLN O 2.03 139.9 119.8 -107.0 1.000 -0.580 core.scoring.hbonds.HBondSet: #A 55 ARG N A 51 TYR O 1.91 145.7 149.7 -119.9 1.000 -0.733 core.scoring.hbonds.HBondSet: #A 56 LYS N A 52 ILE O 2.05 152.8 145.5 -144.7 1.000 -1.268 core.scoring.hbonds.HBondSet: #A 57 MET N A 53 ARG O 1.90 161.7 154.0 -106.5 1.000 -0.970 core.scoring.hbonds.HBondSet: #A 58 THR N A 54 SER O 2.05 153.5 133.7 -110.9 1.000 -0.941 core.scoring.hbonds.HBondSet: #A 59 GLU N A 55 ARG O 2.06 152.9 137.4 -113.4 1.000 -0.939 core.scoring.hbonds.HBondSet: #A 55 ARG NE A 113 LEU O 2.13 147.9 119.9 -95.9 0.859 -0.450 core.scoring.hbonds.HBondSet: #A 55 ARG NH2A 113 LEU O 1.82 143.4 172.4 178.3 0.859 -0.454 core.scoring.hbonds.HBondSet: #A 60 ILE N A 56 LYS O 1.92 158.0 145.1 -109.1 1.000 -0.960 core.scoring.hbonds.HBondSet: #A 56 LYS NZ A 78 TYR O 1.99 147.6 161.9 -149.3 0.976 -0.347 core.scoring.hbonds.HBondSet: #A 61 ALA N A 57 MET O 2.19 141.3 144.0 -107.9 1.000 -0.481 core.scoring.hbonds.HBondSet: #A 62 GLN N A 58 THR O 2.32 147.4 145.9 -134.5 1.000 -0.741 core.scoring.hbonds.HBondSet: #A 63 LYS N A 59 GLU O 2.38 148.8 139.1 -123.6 1.000 -0.599 core.scoring.hbonds.HBondSet: #A 78 TYR OH A 59 GLU OE1 2.33 163.0 127.0 55.3 0.882 -0.201 core.scoring.hbonds.HBondSet: #A 64 LEU N A 60 ILE O 2.21 144.1 134.6 -117.2 1.000 -0.669 core.scoring.hbonds.HBondSet: #A 66 GLU N A 62 GLN O 2.15 126.2 128.1 -135.5 1.000 -0.625 core.scoring.hbonds.HBondSet: #A 102 ARG NH1A 64 LEU O 2.20 150.3 103.2 -43.0 0.859 -0.641 core.scoring.hbonds.HBondSet: #A 69 GLU N A 67 SER OG 1.98 163.8 131.5 73.0 0.459 -2.039 core.scoring.hbonds.HBondSet: #A 77 ARG NH2A 69 GLU OE1 2.08 111.0 127.8 164.8 0.600 -0.556 core.scoring.hbonds.HBondSet: #A 102 ARG NH2A 69 GLU O 1.73 172.3 129.2 104.5 0.647 -0.841 core.scoring.hbonds.HBondSet: #A 74 LEU N A 70 PRO O 2.10 138.8 143.2 -162.9 1.000 -1.132 core.scoring.hbonds.HBondSet: #A 75 ALA N A 71 ILE O 1.85 153.0 140.3 -108.4 1.000 -0.788 core.scoring.hbonds.HBondSet: #A 76 ScoreType.dof_constraintScoreType.branch_connScoreType.linear_branch_connScoreType.rama_preproScoreType.paa_abego3ScoreType.cart_bondedScoreType.cart_bonded_angleScoreType.cart_bonded_lengthScoreType.cart_bonded_ringScoreType.cart_bonded_torsionScoreType.cart_bonded_properScoreType.cart_bonded_improperScoreType.gen_bondedScoreType.gen_bonded_bondScoreType.gen_bonded_angleScoreType.gen_bonded_torsionScoreType.gen_bonded_improperScoreType.neigh_vectScoreType.neigh_countScoreType.neigh_vect_rawScoreType.symE_bonusScoreType.sym_ligScoreType.mhc_epitopeScoreType.pack_statScoreType.rmsScoreType.res_type_constraintScoreType.res_type_linking_constraintScoreType.pocket_constraintScoreType.backbone_stub_constraintScoreType.backbone_stub_linear_constraintScoreType.surfaceScoreType.p_aaScoreType.unfoldedScoreType.split_unfolded_two_bodyScoreType.fa_atr_refScoreType.fa_rep_refScoreType.fa_sol_refScoreType.fa_elec_refScoreType.hbond_refScoreType.dslf_fa13_refScoreType.fa_intra_atr_refScoreType.fa_intra_rep_refScoreType.fa_intra_sol_refScoreType.pro_close_refScoreType.fa_dun_refScoreType.fa_dun_dev_refScoreType.fa_dun_rot_refScoreType.fa_dun_semi_refScoreType.rama_refScoreType.p_aa_pp_refScoreType.omega_refScoreType.mm_lj_intra_rep_refScoreType.mm_lj_intra_atr_refScoreType.mm_twist_refScoreType.elec_dens_fastScoreType.elec_dens_windowScoreType.elec_dens_whole_structure_caScoreType.elec_dens_whole_structure_allatomScoreType.elec_dens_atomwiseScoreType.grid_vdwScoreType.xtal_mlScoreType.xtal_rworkScoreType.xtal_rfreeScoreType.hpatchScoreType.Menv_smoothScoreType.wat_desolvScoreType.ring_closeScoreType.aa_repeatScoreType.aa_compositionScoreType.aspartimide_penaltyScoreType.hbnetScoreType.buried_unsatisfied_penaltyScoreType.netchargeScoreType.voids_penaltyScoreType.sap_constraintScoreType.dna_envScoreType.dna_pairScoreType.dump_trajectoryScoreType.PyRosettaEnergy_firstScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.PyRosettaEnergy_lastScoreType.sidechain_neighborsScoreType.target_clashScoreType.membrane_span_constraintScoreType.membrane_span_term_z_constraintScoreType.aromatic_restraintScoreType.rna_coarse_distScoreType.total_scoreScoreType.dummy_score_type identifying hydrogen bonds in structure GLU N A 72 LEU O 2.12 179.0 157.2 -97.9 1.000 -1.108 core.scoring.hbonds.HBondSet: #A 77 ARG N A 73 TYR O 2.25 145.4 127.3 -111.3 1.000 -0.591 core.scoring.hbonds.HBondSet: #A 78 TYR N A 74 LEU O 2.27 139.7 142.0 -109.7 1.000 -0.357 core.scoring.hbonds.HBondSet: #A 80 PHE N A 75 ALA O 1.93 151.5 158.1 109.3 1.000 -0.785 core.scoring.hbonds.HBondSet: #A 85 THR N A 82 SER OG 2.28 168.9 144.9 9.5 0.482 -0.986 core.scoring.hbonds.HBondSet: #A 86 LEU N A 82 SER O 2.39 154.0 131.8 -121.2 1.000 -0.707 core.scoring.hbonds.HBondSet: #A 87 THR N A 83 GLN O 1.58 162.4 157.0 -131.4 1.000 -0.163 core.scoring.hbonds.HBondSet: #A 88 ARG N A 84 GLN O 1.93 164.6 148.5 -104.7 1.000 -1.041 core.scoring.hbonds.HBondSet: #A 89 THR N A 85 THR O 2.15 160.7 139.8 -119.7 1.000 -1.116 core.scoring.hbonds.HBondSet: #A 90 PHE N A 86 LEU O 1.84 164.3 149.9 -87.9 1.000 -0.895 core.scoring.hbonds.HBondSet: #A 91 LYS N A 87 THR O 2.05 156.2 143.4 -111.4 1.000 -0.976 core.scoring.hbonds.HBondSet: #A 92 ASN N A 88 ARG O 2.11 145.3 137.3 -113.7 1.000 -0.732 core.scoring.hbonds.HBondSet: #A 93 TYR N A 89 THR O 2.20 132.5 141.4 -131.1 1.000 -0.528 core.scoring.hbonds.HBondSet: #A 93 TYR N A 90 PHE O 2.17 133.3 101.2 -94.2 1.000 -0.015 core.scoring.hbonds.HBondSet: #A 94 PHE N A 90 PHE O 1.91 148.0 158.2 -147.9 1.000 -0.887 core.scoring.hbonds.HBondSet: #A 95 ASP N A 91 LYS O 1.86 129.3 118.4 -77.4 1.000 -0.164 core.scoring.hbonds.HBondSet: #A 93 TYR OH A 111 ARG O 1.83 153.2 166.2 98.5 0.624 -0.510 core.scoring.hbonds.HBondSet: #A 111 ARG NH1A 93 TYR O 2.39 132.6 132.2 -117.9 0.624 -0.001 core.scoring.hbonds.HBondSet: #A 111 ARG NH1A 95 ASP OD2 1.88 140.2 140.4 -85.8 0.435 -0.369 core.scoring.hbonds.HBondSet: #A 111 ARG NH2A 95 ASP OD2 1.97 137.7 130.0 27.8 0.435 -1.037 core.scoring.hbonds.HBondSet: #A 101 TYR N A 97 PRO O 2.06 151.2 145.9 -135.7 1.000 -1.111 core.scoring.hbonds.HBondSet: #A 102 ARG N A 98 PRO O 2.03 134.2 138.7 -133.9 1.000 -0.762 core.scoring.hbonds.HBondSet: #A 103 MET N A 99 HIS O 2.13 143.0 152.2 -153.1 1.000 -0.914 core.scoring.hbonds.HBondSet: #A 112 PHE N A 109 GLU O 2.04 153.8 151.0 -144.0 1.000 -1.177 core.scoring.hbonds.HBondSet: #A 114 HIS NE2A 109 GLU OE2 2.35 163.9 126.7 64.4 0.388 -0.463 core.scoring.hbonds.HBondSet: #A 116 LEU N A 114 HIS O 1.65 145.1 121.9 -164.6 1.000 -1.004 Finished T200_Scoring in 0:00:09.453092